[gmx-users] Tutorial

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 18 20:19:11 CEST 2011

Sara baretller wrote:
> Hi justin
> in the tutorail you have
> It is not necessary to run a complete energy minimization procedure on 
> the bilayer, although you can if you want. The .tpr file contains 
> information about bonding and periodicity, so it can, in a sense, be 
> used to reconstruct "broken" molecules.
> when i tried using the minimized gro file i go this error
> Fatal error:
> Structure or trajectory file has more atoms (3655) than the topology (1792)
> For more information and tips for troubleshooting, please check the GROMACS

The contents of your topology do not match the structure file.  I don't know 
what's wrong.  Presumably, if you have created a .tpr file to do energy 
minimization, you have a self-consistent coordinate file and topology.  Either 
you're using the wrong files or you've made a modification to the topology that 
has messed it up.  I can't guess which.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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